Define linkage groups based on the:

Use the radio buttons to specify an option for defining linkage groups.

Available options are listed in the table below:

Options:	Choose this option:
Number of Linkage Groups	When you want to form an exact number of clusters. The automated hierarchical clustering algorithm will assign markers into groups until the number of groups equals the value specified using the Number of Linkage Groups parameter.
Recombination Fraction Cutoff	When you want to cluster markers based on a recombination fraction cutoff. The clustering algorithm compares groups (either based on average recombination distance between groups, maximum recombination, or minimum recombination) and will join markers into groups until the threshold specified using the Recombination Fraction Cutoff parameter is met.

To Specify How Linkage Groups are to be Defined:

Make sure that Automated Hierarchical Clustering is specified for Choose a linkage grouping method .

Make a selection using the drop-down menu.